3vta - Revision history

OCA at 19:03, 27 July 2022

OCA — Wed, 27 Jul 2022 19:03:01 GMT

←Older revision		Revision as of 19:03, 27 July 2022
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	==Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L==		==Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L==
-	<StructureSection load='3vta' size='340' side='right' caption='[[3vta]], [[Resolution\|resolution]] 2.75Å' scene=''>	+	<StructureSection load='3vta' size='340' side='right'caption='[[3vta]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vta]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Cucumis_melo Cucumis melo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VTA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vta]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cucumis_melo Cucumis melo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VTA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DFP:DIISOPROPYL+PHOSPHONATE'>DFP</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DFP:DIISOPROPYL+PHOSPHONATE'>DFP</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Cucumisin Cucumisin], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.25 3.4.21.25] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cucumisin Cucumisin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.25 3.4.21.25] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3vta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vta OCA], [~~http~~://pdbe.org/3vta PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vta RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vta PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vta ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vta OCA], [https://pdbe.org/3vta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vta RCSB], [https://www.ebi.ac.uk/pdbsum/3vta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vta ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	[[Category: Cucumis melo]]		[[Category: Cucumis melo]]
	[[Category: Cucumisin]]		[[Category: Cucumisin]]
		+	[[Category: Large Structures]]
	[[Category: Arima, K]]		[[Category: Arima, K]]
	[[Category: Hosaka, T]]		[[Category: Hosaka, T]]

OCA at 11:27, 4 August 2016

OCA — Thu, 04 Aug 2016 11:27:44 GMT

←Older revision		Revision as of 11:27, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L==		==Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L==
	<StructureSection load='3vta' size='340' side='right' caption='[[3vta]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='3vta' size='340' side='right' caption='[[3vta]], [[Resolution\|resolution]] 2.75Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DFP:DIISOPROPYL+PHOSPHONATE'>DFP</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DFP:DIISOPROPYL+PHOSPHONATE'>DFP</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cucumisin Cucumisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.25 3.4.21.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cucumisin Cucumisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.25 3.4.21.25] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vta OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vta RCSB], [http://www.ebi.ac.uk/pdbsum/3vta PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vta OCA], [http://pdbe.org/3vta PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vta RCSB], [http://www.ebi.ac.uk/pdbsum/3vta PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vta ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3vta" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:06, 21 December 2014

OCA — Sun, 21 Dec 2014 07:06:08 GMT

←Older revision		Revision as of 07:06, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3vta\| PDB=3vta \| SCENE= }}~~	+	==Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L==
-	===Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L===	+	<StructureSection load='3vta' size='340' side='right' caption='[[3vta]], [[Resolution\|resolution]] 2.75Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22841692}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3vta]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cucumis_melo Cucumis melo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VTA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DFP:DIISOPROPYL+PHOSPHONATE'>DFP</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cucumisin Cucumisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.25 3.4.21.25] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vta OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vta RCSB], [http://www.ebi.ac.uk/pdbsum/3vta PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cucumisin is a plant serine protease, isolated as an extracellular glycoprotein from the melon fruit Cucumis melo L. var. Prince. Cucumisin is composed of multiple domain modules, including catalytic, protease-associated, and fibronectin-III-like domains. The crystal structure of cucumisin was determined by the multiwavelength anomalous dispersion method and refined at 2.75A resolution. A structural homology search indicated that the catalytic domain of cucumisin shares structural similarity with subtilisin and subtilisin-like fold enzymes. According to the Z-score, the highest structural similarity is with tomato subtilase 3 (SBT3), with an rmsd of 3.5A for the entire region. The dimer formation mediated by the protease-associated domain in SBT3 is a distinctive structural characteristic of cucumisin. On the other hand, analytical ultracentrifugation indicated that cucumisin is mainly monomeric in solution. Although the locations of the amino acid residues composing the catalytic triad are well conserved between cucumisin and SBT3, a disulfide bond is uniquely located near the active site of cucumisin. The steric circumstances of the active site with this disulfide bond are distinct from those of SBT3, and it contributes to the substrate preference of cucumisin, especially at the P2 position. Among the plant serine proteases, the thermostability of cucumisin is higher than that of its structural homologue SBT3, as determined by their melting points. A structural comparison between cucumisin and SBT3 revealed that cucumisin possesses less surface area and shortened loop regions. Consequently, the higher thermostability of cucumisin is achieved by its more compact structure.

-	~~==About this Structure==~~	+	Crystal structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L.,Murayama K, Kato-Murayama M, Hosaka T, Sotokawauchi A, Yokoyama S, Arima K, Shirouzu M J Mol Biol. 2012 Oct 26;423(3):386-96. doi: 10.1016/j.jmb.2012.07.013. Epub 2012 , Jul 24. PMID:22841692<ref>PMID:22841692</ref>
-	~~[[3vta]] is a 2 chain~~ structure ~~with sequence~~ from ~~[http://en.wikipedia.org/wiki/Cucumis_melo~~ Cucumis melo]. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=3VTA OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:022841692</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Cucumis melo]]		[[Category: Cucumis melo]]
	[[Category: Cucumisin]]		[[Category: Cucumisin]]
-	[[Category: Arima, K.]]	+	[[Category: Arima, K]]
-	[[Category: Hosaka, T.]]	+	[[Category: Hosaka, T]]
-	[[Category: Kato-Murayama, M.]]	+	[[Category: Kato-Murayama, M]]
-	[[Category: Murayama, K.]]	+	[[Category: Murayama, K]]
-	[[Category: Shirouzu, M.]]	+	[[Category: Shirouzu, M]]
-	[[Category: Sotokawauchi, A.]]	+	[[Category: Sotokawauchi, A]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Serine protease]]		[[Category: Serine protease]]
	[[Category: Subtilisin-like fold]]		[[Category: Subtilisin-like fold]]

OCA at 11:00, 24 July 2013

OCA — Wed, 24 Jul 2013 11:00:31 GMT

←Older revision		Revision as of 11:00, 24 July 2013
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-	[[Image:3vta.jpg\|left\|200px]]
-
	{{STRUCTURE_3vta\| PDB=3vta \| SCENE= }}		{{STRUCTURE_3vta\| PDB=3vta \| SCENE= }}
-
	===Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L===		===Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L===
-		+	{{ABSTRACT_PUBMED_22841692}}

	==About this Structure==		==About this Structure==
	[[3vta]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cucumis_melo Cucumis melo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTA OCA].		[[3vta]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cucumis_melo Cucumis melo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTA OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022841692</ref><references group="xtra"/><references/>
	[[Category: Cucumis melo]]		[[Category: Cucumis melo]]
	[[Category: Cucumisin]]		[[Category: Cucumisin]]

OCA at 05:30, 8 August 2012

OCA — Wed, 08 Aug 2012 05:30:01 GMT

←Older revision		Revision as of 05:30, 8 August 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3vta.jpg\|left\|200px]]

-	~~The entry~~ 3vta ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3vta\| PDB=3vta \| SCENE= }}

-	~~Authors: Murayama~~, ~~K., Kato~~-~~Murayama, M., Hosaka, T., Sotokawauchi, A., Shirouzu, M., Arima, K., Yokoyama, S.~~	+	===Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L===

-	~~Description: Crystal~~ Structure ~~of cucumisin,~~ a ~~subtilisin-like endoprotease~~ from Cucumis melo L	+
		+	==About this Structure==
		+	[[3vta]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cucumis_melo Cucumis melo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTA OCA].
		+	[[Category: Cucumis melo]]
		+	[[Category: Cucumisin]]
		+	[[Category: Arima, K.]]
		+	[[Category: Hosaka, T.]]
		+	[[Category: Kato-Murayama, M.]]
		+	[[Category: Murayama, K.]]
		+	[[Category: Shirouzu, M.]]
		+	[[Category: Sotokawauchi, A.]]
		+	[[Category: Yokoyama, S.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Serine protease]]
		+	[[Category: Subtilisin-like fold]]

OCA at 07:13, 20 June 2012

OCA — Wed, 20 Jun 2012 07:13:36 GMT

←Older revision		Revision as of 07:13, 20 June 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3vta is ON HOLD	+	The entry 3vta is ON HOLD until Paper Publication

	Authors: Murayama, K., Kato-Murayama, M., Hosaka, T., Sotokawauchi, A., Shirouzu, M., Arima, K., Yokoyama, S.		Authors: Murayama, K., Kato-Murayama, M., Hosaka, T., Sotokawauchi, A., Shirouzu, M., Arima, K., Yokoyama, S.

	Description: Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L		Description: Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L

OCA at 05:36, 13 June 2012

OCA — Wed, 13 Jun 2012 05:36:38 GMT

←Older revision		Revision as of 05:36, 13 June 2012
Line 3:		Line 3:
	The entry 3vta is ON HOLD		The entry 3vta is ON HOLD

-	Authors: Murayama, K, Kato-Murayama, M, Hosaka, T, Sotokawauchi, A, Shirouzu, M, Arima, K, Yokoyama, S	+	Authors: Murayama, K., Kato-Murayama, M., Hosaka, T., Sotokawauchi, A., Shirouzu, M., Arima, K., Yokoyama, S.

-	Description: Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L.	+	Description: Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L

OCA: Protected "3vta" [edit=sysop:move=sysop]

OCA — Wed, 30 May 2012 05:19:02 GMT

Protected "3vta" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:19, 30 May 2012

OCA: New page: '''Unreleased structure''' The entry 3vta is ON HOLD Authors: Murayama, K, Kato-Murayama, M, Hosaka, T, Sotokawauchi, A, Shirouzu, M, Arima, K, Yokoyama, S Description: Crystal Structu...

OCA — Wed, 30 May 2012 05:19:01 GMT

New page: '''Unreleased structure''' The entry 3vta is ON HOLD Authors: Murayama, K, Kato-Murayama, M, Hosaka, T, Sotokawauchi, A, Shirouzu, M, Arima, K, Yokoyama, S Description: Crystal Structu...

New page

'''Unreleased structure'''

The entry 3vta is ON HOLD

Authors: Murayama, K, Kato-Murayama, M, Hosaka, T, Sotokawauchi, A, Shirouzu, M, Arima, K, Yokoyama, S

Description: Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L.